There is a way you can get around this problem. The way I would do it is to make the pc spawn in a new module which you won't be able to see because a computer terminal style dialog will start when you enter. The dialog will pretty much ask you hey do you want to play The Sith Lords or The Jedi Master? Then whatever option you choose it will take you to the damaged Ebon Hawk or the first module of TJM.

If you did it this way, wouldn't that come after the opening Star Wars title crawl and intro movie? I think that having separate folders for TSL and TJM is the easier way.